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WORKFLOW: Pilon
Rauf Salamzade edited this page Dec 22, 2020
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The Pilon workflow simplifies running Pilon based variant calling analysis.
| Parameter Identifier | Parameter Value Type / Default | Parameter Description |
|---|---|---|
| reference_fasta | String. None | Path to reference genome FASTA. In the same directory as the FASTA file should be representative bwa index files. To ensure things run smoothly please run bwa using its installation in the conda environment main_env. |
| pilon_options | String. --variant | Specify options for running Pilon. |
| run_cleanup | Boolean. False | Delete intermediate FASTQ files: True/False |